RnoINT0071670 @ rn6
Intron Retention
Gene
ENSRNOG00000001587 | Hoxd12
Description
homeo box D12 [Source:RGD Symbol;Acc:1309797]
Coordinates
chr3:61597382-61598503:+
Coord C1 exon
chr3:61597382-61598024
Coord A exon
chr3:61598025-61598182
Coord C2 exon
chr3:61598183-61598503
Length
158 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
GGGTCGGGGCTCTGTTTCAGGCC
3' ss Score
5.26
Exon sequences
Seq C1 exon
CCTCTGAGCCGGTCCTCTTATTCCGGGTTGTAACTAAATACTGTTGCTGAGCACAGCCGAGGCCCTTTGTTGGAGATGTGTGAGCGCAGTCTCTACAGAGCTGGCTATGTGGGCTCGCTTCTGAATTTACAGTCACCGGACTCTTTCTACTTTTCTAACCTGCGACCCAATGGCAGCCAGTTGGCCGCACTTCCCCCCATCTCATACCCTCGCAGCGCTCTGCCCTGGGCCGCTACGCCCGCCTCGTGCACCCCTGCGCAGCCTACCACCGCCTCTGCCTTTGGGGGCTTCTCTCAGCCGTACTTGACCGGCTCTGGGCCCATTGGCCTGCAGTCTCCAGGCACCAAAGACGGACCCGAAGACCAGGTCAAGTTCTATACGCCTGATGCGGCCACTGCATCTGAGGAACGCAGCCGGACTAGGCCGCCCTTCGCCCCCGAGTCTAGCCTGGTTCACTCGGCTCTCAAAGGCACCAAGTACGACTTCGCGGGTGTGGGCCGAGCCGCTCCAGGCTCTGTGACCCTGCTCCAGGGGGCCCCCTGCGCCTCCAACTTCAAGGAAGACACCAAAGGCCCGCTCAACTTGAACATGGCAGTGCAAGTGGCCGGGGTGGCCTCGTGCCTGCGATCTTCGCTGCCCGACG
Seq A exon
GTAAACGGTGCCCAAACTCCCCAAGCCGGTTTAGGCAGGGACGGGAGGTGGGATATCAGGGACAGTTGTACAGGGAGGAGAACGGTCAGCAGTGGTGAACCTCTGTGGGGCGGGCAGTTGATCTGAGCGAGCTGACATGGGTCGGGGCTCTGTTTCAG
Seq C2 exon
GCCTGCCATGGGGGGCGGCCCCGGGGAGGGCCCGCAAGAAGAGGAAACCATACACAAAGCAACAGATTGCGGAGCTGGAGAATGAATTCCTGGTCAATGAATTCATCAACCGGCAGAAACGTAAGGAATTGTCCAACAGGCTGAACCTCAGCGACCAGCAGGTCAAAATCTGGTTCCAGAACCGGCGTATGAAGAAGAAGCGTGTGGTGCAGCGCGAGCAAGCACTGGCGCTCTACTAGCTGCCCACGGGGCTGAGGCCTTGCCAAGCCTGCCCTTTTGGACCGAGGCCTGGCTGTGGAGGAGGTGTTGGGGCTGGAGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001587:ENSRNOT00000068636:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.305 A=NA C2=0.241
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTCACTCGGCTCTCAAAGG
R:
ATGGTTTCCTCTTCTTGCGGG
Band lengths:
245-403
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]